341 Works

Data from: CO2 alters community composition and response to nutrient enrichment of freshwater phytoplankton

Etienne Low-Décarie, Gregor F. Fussmann & Graham Bell
Nutrients can limit the productivity of ecosystems and control the composition of the communities of organisms that inhabit them. Humans are causing atmospheric CO2 concentrations to reach levels higher than those of the past millions of years while at the same time propagating eutrophication through the addition of nutrients to lakes and rivers. We studied the effect of elevated CO2 concentrations, nutrient addition and their interaction in a series of freshwater mesocosm experiments using a...

Data from: A review of riverine ecosystem service quantification: research gaps and recommendations

Dalal E. L. Hanna, Stephanie A. Tomscha, Camille Ouellet Dallaire & Elena M. Bennett
1.Increasing demand for benefits provided by riverine ecosystems threatens their sustainable provision. The ecosystem service concept is a promising avenue to inform riverine ecosystem management, but several challenges have prevented the application of this concept. 2.We quantitatively assess the field of riverine ecosystem services’ progress in meeting these challenges. We highlight conceptual and methodological gaps, which have impeded integration of the ecosystem service concept into management. 3.Across 89 relevant studies, 33 unique riverine ecosystem services...

Data from: Evolutionary rescue of sexual and asexual populations in a deteriorating environment

Josianne Lachapelle & Graham Bell
The environmental change experienced by many contemporary populations of organisms poses a serious risk to their survival. From the theory of evolutionary rescue we predict that the combination of sex and genetic diversity should increase the probability of survival by increasing variation and thereby the probability of generating a type that can tolerate the stressful environment. We tested this prediction by comparing experimental populations of Chlamydomonas reinhardtii that differ in sexuality and in the initial...

Data from: Evolutionary inferences from the analysis of exchangeability

Andrew P. Hendry, Renaud Kaeuffer, Erika Crispo, Catherine Lynn Peichel & Daniel I. Bolnick
Evolutionary inferences are usually based on statistical models that compare mean genotypes and phenotypes (or their frequencies) among populations. An alternative is to use the actual distribution of genotypes and phenotypes to infer the “exchangeability” of individuals among populations. We illustrate this approach by using discriminant functions on principal components to classify individuals among paired lake and stream populations of threespine stickleback in each of six independent watersheds. Classification based on neutral and non-neutral microsatellite...

Data from: INTREPAD: a randomized trial of naproxen to slow progress of presymptomatic Alzheimer disease

Pierre-Francois Meyer, Jennifer Tremblay-Mercier, Jeannie Leoutsakos, Cecile Madjar, Marie-Elyse Lafaille-Magnan, Melissa Savard, Pedro Rosa-Neto, Judes Poirier, Pierre Etienne & John Breitner
Objective: Evaluate the safety and efficacy of low-dose naproxen for prevention of progression in pre-symptomatic AD among cognitively intact persons at-risk. Methods: INTREPAD, a two-year double-masked pharmaco-prevention trial, enrolled 195 AD family history-positive elderly (mean age 63 years) screened carefully to exclude cognitive disorder. These were randomized 1:1 to naproxen sodium 220mg twice-daily or placebo. Multimodal imaging, neurosensory, cognitive and (in ~50%) CSF biomarker evaluations were performed at Baseline, 3, 12, and 24 months. A...

Data from: Quantifying climate sensitivity and climate-driven change in North American amphibian communities

David A. W. Miller, Evan H. Campbell Grant, Erin Muths, Staci M. Amburgey, Michael J. Adams, Maxwell B. Joseph, J. Hardin Waddle, Pieter T. J. Johnson, Maureen E. Ryan, Benedikt R. Schmidt, Daniel L. Calhoun, Courtney L. Davis, Robert N. Fisher, David M. Green, Blake R. Hossack, Tracy A. G. Rittenhouse, Susan C. Walls, Larissa L. Bailey, Sam S. Cruickshank, Gary M. Fellers, Thomas A. Gorman, Carola A. Haas, Ward Hughson, David S. Pilliod, Steven J. Price … & Brent H. Sigafus
Changing climate will impact species’ ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local...

Data from: One-locus-several-primers: a strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

Emmanuel Corse, Christelle Tougard, Gaït Archambaud-Suard, Jean-François Agnèse, Françoise D. Messu Mandeng, Charles F. Bilong Bilong, David Duneau, Lucie Zinger, Rémi Chappaz, Charles C. Y. Xu, Emese Meglécz & Vincent Dubut
In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both...

Data from: Projected polar bear sea ice habitat in the Canadian Arctic Archipelago

Stephen G. Hamilton, Laura Castro De La Guardia, Andrew E. Derocher, Vicki Sahanatien, Bruno Tremblay & David Huard
Background: Sea ice across the Arctic is declining and altering physical characteristics of marine ecosystems. Polar bears (Ursus maritimus) have been identified as vulnerable to changes in sea ice conditions. We use sea ice projections for the Canadian Arctic Archipelago from 2006 – 2100 to gain insight into the conservation challenges for polar bears with respect to habitat loss using metrics developed from polar bear energetics modeling. Principal Findings: Shifts away from multiyear ice to...

Data from: Vegetation response to control of invasive Tamarix in southwestern US rivers: a collaborative study including 416 sites

Eduardo González, Anna A. Sher, Robert M. Anderson, Robin F. Bay, Daniel W. Bean, Gabriel J. Bissonnete, Bérenger Bourgeois, David J. Cooper, Kara Dohrenwend, Kim D. Eichhorst, Hisham El Waer, Deborah K. Kennard, Rebecca Harms-Weissinger, Annie L. Henry, Lori J. Makarick, Steven M. Ostoja, Lindsay V. Reynolds, W. Wright Robinson & Patrick B. Shafroth
Most studies assessing vegetation response following control of invasive Tamarix trees along southwestern U.S. rivers have been small in scale (e.g., river reach), or at a regional scale but with poor spatial-temporal replication, and most have not included testing the effects of a now widely-used biological control. We monitored plant composition following Tamarix control along hydrologic, soil and climatic gradients in 244 treated and 172 reference sites across six U.S. States. This represents the largest...

Data from: Global macroevolution and macroecology of passerine song

William David Pearse, Ignacio Morales-Castilla, Logan S. James, Maxwell Farrell, Frédéric Boivin & T. Jonathan Davies
Studying the macroevolution of the songs of Passeriformes (perching birds) has proved challenging. The complexity of the task stems not just from the macroevolutionary and macroecological challenge of modelling so many species, but also from the difficulty in collecting and quantifying birdsong itself. Using machine learning techniques, we extracted songs from a large citizen science dataset, and then analysed the evolution, and biotic and abiotic predictors of variation in birdsong across 578 passerine species. Contrary...

Data from: Developmental plasticity of the stress response in female but not male guppies

Laura Chouinard-Thuly, Adam R. Reddon, Ioannis Leris, Ryan L. Earley & Simon M. Reader
To survive, animals must respond appropriately to stress. Stress responses are costly, so early-life experiences with potential stressors could adaptively tailor adult stress responses to local conditions. However, how multiple stressors influence the development of the stress response remains unclear, as is the role of sex. Trinidadian guppies (Poecilia reticulata) are small fish with extensive life history differences between the sexes and population variation in predation pressure and social density. We investigated how sex and...

Data from: Predicting peatland carbon fluxes from non-destructive plant traits

Ellie M. Goud, Tim R. Moore & Nigel T. Roulet
1. Determining the plant traits that best predict carbon (C) storage is increasingly important as global change drivers will affect plant species composition and ecosystem C cycling. Despite the critical role of peatlands in the global C cycle, trait-flux relationships in peatlands are relatively unknown. 2. We assessed the ability of four non-destructive plant traits to predict carbon dioxide (CO2) and methane (CH4) fluxes over two growing seasons in a temperate peatland in Ontario, Canada....

Data from: Age and early social environment influence guppy social learning propensities

Ioannis Leris & Simon M. Reader
Social learning, learning from others, allows animals to quickly and adaptively adjust to changing environments, but only if social learning provides reliable, useful information in that environment. Early life conditions provide a potential cue to the reliability of social information later in life. Here, we addressed whether direct early life experience of the utility of social learning influences later social learning propensities. We reared guppy, Poecilia reticulata, fry for 45 days in three different social...

Data from: Effects of Lewy body disease and Alzheimer’s disease on brain atrophy and cognitive dysfunction

Sung Woo Kang, Seun Jeon, Han Soo Yoo, Seok Jong Chung, Phil Hyu Lee, Young H. Sohn, Mijin Yun, Alan C. Evans & Byoung Seok Ye
Objectives: We investigated the independent and interaction effects of Alzheimer’s disease (AD) and Lewy body disease (LBD) on cognition and brain atrophy. Methods: We consecutively recruited 38 controls and 108 patients with AD-related cognitive impairment (ADCI) and/or LBD-related cognitive impairment (LBCI) from university-based dementia and movement clinics. Diagnoses of ADCI and LBCI were supported by 18F-Florbetaben PET and 18F-FP-CIT-PET, respectively. There were 38 controls, 26 patients with pure ADCI (18 mild cognitive impairment (MCI) and...

Data from: Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community

Torrey W. Rodgers, Charles C. Y. Xu, Jacalyn Giacalone, Karen M. Kapheim, Kristin Saltonstall, Marta Vargas, Douglas W. Yu, Panu Somervuo, W. Owen McMillan & Patrick A. Jansen
Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera-trapping. We collected 1084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For...

Data from: The ecology and evolution of seed predation by Darwin's finches on Tribulus cistoides on the Galápagos Islands

Sofía Carvajal-Endara, Andrew P. Hendry, Nancy C. Emery, Corey P. Neu, Diego Carmona, Kiyoko M. Gotanda, T. Jonathan Davies, Jaime A. Chaves & Marc T. J Johnson
Predator-prey interactions play a key role in the evolution of species traits through antagonistic coevolutionary arms-races. The evolution of beak morphology in the Darwin’s finches in response to competition for seed resources is a classic example of evolution by natural selection. The seeds of Tribulus cistoides are an important food source for the largest ground finch species (Geospiza fortis, G. magnirostris, and G. conirostris) in dry months, and the hard spiny morphology of the fruits...

Data from: Phylogenetic conservatism in plant phenology

T. Jonathan Davies, Elizabeth M. Wolkovich, Nathan J. B. Kraft, Nicolas Salamin, Jenica M. Allen, Toby R. Ault, Julio L. Betancourt, Kjell Bolmgren, Elsa E. Cleland, Benjamin I. Cook, Theresa M. Crimmins, Susan J. Mazer, Gregory J. McCabe, Stephanie Pau, Jim Regetz, Mark D. Schwartz & Steven E. Travers
Phenological events – defined points in the life cycle of a plant or animal – have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism – the tendency...

Data from: Effects of spatial scale of sampling on food web structure

Spencer A. Wood, Roly Russell, Dieta Hanson, Richard J. Williams & Jennifer A. Dunne
This study asks whether the spatial scale of sampling alters structural properties of food webs and whether any differences are attributable to changes in species richness and connectance with scale. Understanding how different aspects of sampling effort affect ecological network structure is important for both fundamental ecological knowledge and the application of network analysis in conservation and management. Using a highly resolved food web for the marine intertidal ecosystem of the Sanak Archipelago in the...

Data from: Climate mediates the effects of disturbance on ant assemblage structure

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Simon Watson, Manoli Photakis, Silvia Abril, Alan N. Andersen, Elena Angulo, Inge Armbrecht, Xavier Arnan, Fabricio B. Baccaro, Tom R. Bishop, Raphael Boulay, Cristina Castracani, Israel Del Toro, Thibaut Delsinne, Mireia Diaz, David A. Donoso, Martha L. Enríquez, Tom M. Fayle, Donald H. Feener, Matthew C. Fitzpatrick, Crisanto Gómez, Donato A. Grasso, Sarah Groc … & C. Gomez
Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction...

Data from: It's about time: the temporal dynamics of phenotypic selection in the wild

Adam M. Siepielski, Joseph D. DiBattista & Stephanie M. Carlson
Selection is a central process in nature. Although our understanding of the strength and form of selection has increased, a general understanding of the temporal dynamics of selection in nature is lacking. Here, we assembled a database of temporal replicates of selection from studies of wild populations to synthesize what we do (and do not) know about the temporal dynamics of selection. Our database contains 5519 estimates of selection from 89 studies, including estimates of...

Data from: Comparing fitness and drift explanations of Neanderthal replacement

Dan Shultz, Marcel Montrey & Thomas Shultz
There is a general consensus among archaeologists that replacement of Neanderthals by anatomically modern humans in Europe occurred around 40K to 35K YBP. However, the causal mechanism for this replacement continues to be debated. Searching for specific fitness advantages in the archaeological record has proven difficult, as these may be obscured, absent, or subject to interpretation. Proposed models have therefore featured either fitness advantages in favor of anatomically modern humans, or invoked neutral drift under...

Data from: The evolution of morphological diversity in continental assemblages of Passerine birds

Knud Andreas Jønsson, Jean Philippe Lessard, Robert E. Ricklefs & Jean-Philippe Lessard
Understanding geographic variation in the species richness and lineage composition of regional biotas is a long standing goal in ecology. Why do some evolutionary lineages proliferate while others do not, and how do new colonists fit into an established fauna? Here, we analyse the morphological structure of assemblages of passerine birds in four biogeographic regions to examine the relative influence of colonization history and niche-based processes on regional communities of passerine birds. Using morphological traits...

Data from: Phylogenetic diversity patterns in Himalayan forests reveal evidence for environmental filtering of distinct lineages

Stephanie Shooner, T. Jonathan Davies, Purabi Saikia, Jyotishman Deka, Sanjeeb Bharali, Om Prakash Tripathi, Lalbihari Singha, Mohammed Latif Khan & Selvadurai Dayanandan
Large‐scale environmental gradients have been invaluable for unraveling the processes shaping the evolution and maintenance of biodiversity. Environmental gradients provide a natural setting to test theories about species diversity and distributions within a landscape with changing biotic and abiotic interactions. Elevational gradients are particularly useful because they often encompass a large climatic range within a small geographical extent. Here, we analyzed tree communities in plots located throughout Arunachal Pradesh, a province in northeast India located...

Supplement: Multicenter validated detection of focal cortical dysplasia using deep learning

Ravnoor S Gill, Hyo M Lee, Benoit Caldairou, Seok-Jun Hong, Carmen Barba, Francesco Deleo, Ludovico D’Incerti, Vanessa C Mendes Coelho, Matteo Lenge, Mira Semmelroch, Dewi Schrader, Fabrice Bartolomei, Maxime Guye, Andreas Schulze-Bonhage, Horst Urbach, Kyoo Ho Cho, Fernando Cendes, Renzo Guerrini, Graeme Jackson, R Edward Hogan, Neda Bernasconi & Andrea Bernasconi
Objective. To test the hypothesis that a multicenter-validated computer deep learning algorithm detects MRI-negative focal cortical dysplasia (FCD). Methods. We used clinically acquired 3D T1-weighted and 3D FLAIR MRI of 148 patients (median age, 23 years [range, 2-55]; 47% female) with histologically verified FCD at nine centers to train a deep convolutional neural network (CNN) classifier. Images were initially deemed as MRI-negative in 51% of cases, in whom intracranial EEG determined the focus. For risk...

Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes

Joanne Littlefair, Lee Hrenchuk, Paul Blanchfield, Michael Rennie & Melania Cristescu
Significant advances have been made towards surveying animal and plant communities using DNA isolated from environmental samples. Despite rapid progress, we lack a comprehensive understanding of the “ecology” of environmental DNA (eDNA), particularly its temporal and spatial distribution and how this is shaped by abiotic and biotic processes. Here, we tested how seasonal variation in thermal stratification and animal habitat preferences influence the distribution of eDNA in lakes. We sampled eDNA depth profiles of five...

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